diff --git a/CHANGELOG.md b/CHANGELOG.md index b5ec62785f2fdf3cb3723bde6250b0bd5a9c3238..731991c23b0b693399a339d4a9515a4877ba90ae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,13 +5,12 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/) and this project adheres to [Semantic Versioning](http://semver.org/). -## [1.0.0-rc+7] - 2023-03-28 +## [1.0.0-rc+7] - 2023-03-30 ### Changed - - Add parameter for publicURL - Update opensilex version to 1.0.0-rc+7 -- Add first version of extra module management +- Add first version of extra module management (sixtine, vitioeno) - Add theme and custom configuration ## [1.0.0-rc+6] - 2022-12-19 diff --git a/README.md b/README.md index 81178483e062b538ca15ac04bc092de247b67579..42bedb7619917ac1fd829496ad7a11c7be988b6e 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ Docker compose environnent to deploy opensilex stack based on a previous work <a - [Fresh new install (compose v2)](#fresh-new-install-compose-v2) - [Run minimal opensilex docker stack compose](#run-minimal-opensilex-docker-stack-compose) - [(First install only) Create an administrator user](#first-install-only-create-an-administrator-user) - - [Stop docker stack](#stop-docker-stack) + - [Stop opensilex docker](#stop-opensilex-docker) - [Other tools or customizations](#other-tools-or-customizations) - [(Optional) Add a gui for opensilex-docker-mongodb](#optional-add-a-gui-for-opensilex-docker-mongodb) - [(Optional) Add a reverse proxy](#optional-add-a-reverse-proxy) @@ -23,7 +23,8 @@ Docker compose environnent to deploy opensilex stack based on a previous work <a - [From previous version 1.0.0-rc+5.2 (compose v2)](#from-previous-version-100-rc52-compose-v2) - [From previous version 1.0.0-rc+5.1 (compose v1)](#from-previous-version-100-rc51-compose-v1) - [From previous version before 1.0.0-rc+5.1 (compose v1)](#from-previous-version-before-100-rc51-compose-v1) - - [Customize docker configuration](#customize-docker-configuration) + - [Configure docker configuration](#configure-docker-configuration) + - [Customize opensilex configuration](#customize-opensilex-configuration) - [Modular extensions](#modular-extensions) - [Explanation of modules directory](#explanation-of-modules-directory) - [Configuration for inrae sixtine vigne](#configuration-for-inrae-sixtine-vigne) @@ -32,6 +33,7 @@ Docker compose environnent to deploy opensilex stack based on a previous work <a - [Import (Experimental)](#import-experimental) - [Manage docker](#manage-docker) - [Debug installation](#debug-installation) + - [Stop docker stack](#stop-docker-stack) - [Danger Zone](#danger-zone) - [Stop docker stack and erase all data (Be sure to delete all data)](#stop-docker-stack-and-erase-all-data-be-sure-to-delete-all-data) - [Acknowledgments](#acknowledgments) @@ -144,12 +146,12 @@ Expected configuration :  -## Stop docker stack +## Stop opensilex docker This command will stop the stack. ```bash -docker compose --env-file opensilex.env stop +docker stop opensilex-docker-opensilexapp ``` ## Other tools or customizations @@ -236,7 +238,7 @@ docker stop opensilex && docker rm opensilex docker stop rdf4j && docker rm rdf4j ``` -## Customize docker configuration +## Configure docker configuration Configure `opensilex.env` file to configure opensilex sparql config, applications ports, applications volumes @@ -252,6 +254,7 @@ BASEURIALIAS=opensilex-sandbox # customize path prefix Ex : localhost:8081/opensilex or localhost:8081/phenotyping_si OPENSILEX_PATH_PREFIX=sandbox VERSION_LABEL=test-version +OPENSILEX_PUBLIC_URL=http://localhost:28081/ # public url for web api # FILE SYSTEM # Default value is "gridfs" - Only "gridfs" or "local" are supported @@ -298,22 +301,55 @@ OPENSILEX_CONFIG_HEADERCOMPONENT=opensilex-DefaultHeaderComponent #OPENSILEX_CONFIG_HEADERCOMPONENT=inrae-sixtine-vigne-SixtineHeaderComponent ``` +## Customize opensilex configuration + +Configure `config/opensilex-custom-config.yml` file to activate [custom features](https://github.com/OpenSILEX/opensilex/tree/master/opensilex-doc/src/main/resources/installation/configuration). + +Example : Activate and calculated metrics each 2 hours. + +```bash + +# ------------------------------------------------------------------------------ +# Configuration for module: CoreModule (CoreConfig) +core: + # Metrics options (MetricsConfig) + metrics: + # Activate access metrics (boolean) + enableMetrics: true + # Metrics configs about system (SystemMetricsConfig) + system: + # First metrics for any time depending on is time unit (int) + timeBeforeFirstMetric: 1 + # Delay between whole system metrics (combined with corresponding TimeUnit) (int) + delayBetweenMetrics: 2 + # Default metrics units : DAYS, HOURS, MINUTES, SECONDS are authorized (String) + metricsTimeUnit: HOURS + # Metrics configs about experiments (ExperimentsMetricsConfig) + experiments: + # First metrics for any time depending on is time unit (int) + timeBeforeFirstMetric: 1 + # Delay between whole system metrics (combined with corresponding TimeUnit) (int) + delayBetweenMetrics: 2 + # Default metrics units : DAYS, HOURS, MINUTES, SECONDS are authorized (String) + metricsTimeUnit: HOURS +``` + ## Modular extensions ### Explanation of modules directory -Module (opensilex jar) can be added to *"modules"* directory (opensilex-docker-compose/modules) in order to be deployed in opensilex stack. +Module (opensilex jar) can be added to _"modules"_ directory (opensilex-docker-compose/modules) in order to be deployed in opensilex stack. -There is a module example directory working with *"inrae-sixtine-vigne"* module (inrae-sixtine-vigne-1.1.0.jar) that allow you to change ontology and instance front style. +There is a module example directory working with _"inrae-sixtine-vigne"_ module (inrae-sixtine-vigne-1.1.0.jar) that allow you to change ontology and instance front style. It is localised in opensilex-docker-compose/modules_examples/1.0.0-rc+7/inrae-sixtine-vigne-1.1.0.jar. **How to do it ?** -- To activate your module you must copy a module example that have been compiled for a specified opensilex version in *modules* directory. (Ex : the module located in 1.0.0-rc+7/inrae-sixtine-vigne-1.1.0.jar has been compiled for opensilex version 1.0.0-rc+7). It's all. +- To activate your module you must copy a module example that have been compiled for a specified opensilex version in _modules_ directory. (Ex : the module located in 1.0.0-rc+7/inrae-sixtine-vigne-1.1.0.jar has been compiled for opensilex version 1.0.0-rc+7). It's all. ### Configuration for inrae sixtine vigne -By modifying *opensilex.env* file with this following configuration you will be able to change the theme. +By modifying _opensilex.env_ file with this following configuration you will be able to change the theme. ```bash # Example of modification for sixtine vigne module @@ -375,13 +411,21 @@ This command will give you stack trace of the docker build. docker compose --env-file opensilex.env build --build-arg UID=$(id -u) --build-arg GID=$(id -g) > docker_logs/debug.log ``` +## Stop docker stack + +This command will stop the docker stack. + +```bash +docker compose --env-file opensilex.env down +``` + ## Danger Zone $\color{red}{The\ following\ commands\ may\ produce\ a\ loss\ of\ data}$ ### Stop docker stack and erase all data (Be sure to delete all data) -This command will give you stack trace of the docker build. +This command will stop docker stack and erase all data in your databases. ```bash docker compose --env-file opensilex.env down --volumes